Martini 3 OliGomers: A Scalable Approach for Multimers and Fibrils in GROMACS.

ABSTRACT: Martini 3 is a widely used coarse-grained simulation method for large-scale biomolecular simulations. It can be combined with a Go̅ model to realistically describe higher-order protein structures while allowing the folding and unfolding events. However, as of today, this method has largely been used only for individual monomers. In this article, we describe how the Go̅ model can be implemented within the framework of Martini 3 for a multimer system, taking into account both intramolecular and intermolecular interactions in an oligomeric protein system. We demonstrate the method by showing how it can be applied to both structural stability maintenance and assembly/disassembly of protein oligomers, using aquaporin tetramer, insulin dimer, and amyloid-β fibril as examples. We find that additi

SUBMITTER: Korshunova K 

PROVIDER: S-EPMC11391574 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature